1: Underground spaceships detected.
2: Foundation attempts to reach the group that makes the spaceships and is rejected.
3: Greater threat shows up and attempts to get the spaceships.
4: Foundation allies with the group and uses this opportunity to steal stuff.
5: The greater threat was faked, apparently. And now the group is a bit pissed.

1: The ships were built underground, and there are supporting facilities for the spaceships. Hangars, spare parts, etc.
2: Relations between the 2 groups break down, mainly due to the group's unwillingness to let the Foundation reverse-engineer their tech.
3: This "greater threat" is to be an alternate-dimension Foundation hell-bent on helping the world progress, even if it means exposing the world to anomalies.
4: They stole a spaceship and reverse-engineered it. The Foundation didn't want the GoI to find out. The Foundation didn't find out how the GoI got there, or any of their origins.
5: Shit, I forgot to mention that? Right, the Foundation greatly exaggerated the threat.